The once-capped Brazil international, 26, has been a regular fixture for Los Rojiblancos since joining from Deportivo in 2010.
"Last season was the best of my career and right now I feel important in the dressing room," Luis said on the Atletico website.
"I hope to fulfil my contract because Atletico Madrid will return to be where they deserve to be and I'm happy to form part of the history of the club."
Luis came through the ranks at Figueirense in Brazil before spending time on loan at Ajax, Real Madrid and Deportivo, becoming a first-team player for the latter before joining permanently in 2008.
After joining Atletico following their 2010 Europa League triumph, he dislodged former club captain Antonio Lopez from the left-back slot before going on to make 88 appearances in all competitions over two seasons.